I would say that this is not a bioperl fault, but a very specific situation for people trying to install bioperl without the Berkeley db headers intalled.

The problem was not with bioperl itself, but with my Ubuntu installation that it had the libdb4.6 installed but didn't have the Berkeley db headers from libdb-dev.

I posted this entry here just in case someone find similar problems with the DB_File and wonders which package contains the db.h file, and google for it (googling for it show that other people had it in the past). I don't think that this is a common problem so I didn't send it to the bioperl mailing list, but put it here instead for future reference only.

I have installed several times BioPerl from CPAN in diferent machines and I haven't had problems. But this was because they were my working machines so I had all headers files and programs installed. But in this particular case, the machine is a virtual box in my mac that I was setting to create a DAS server therefore there were a lot of things not installed.

For example I needed to install also "libexpat-dev" in order to have the XML::Parser for the installation of the optional bioperl modules that needed it. And also I needed to install GraphViz before installing Bio::Graphics. etc.

Now that we are here I would say that other problem that I had is that I was not able to install bioperl if I selected the installation of Bio-ASN1-EntrezGene. But without it, bioperl install now OK

Thx, I was setting up a bioinfo workstation with a fresh installation of Ubuntu 11.10 and i stuck during bioperl installing and this was exactly the error I was facing. Thank you for the solution. Just one more thing, I was setting up perl modules using cpanm under perlbrew and I was getting "write permissions" errors just during Bioperl installation, so I need to run cpanm --sudo to work even if the module was installed in home directory.